Photizo example tutorial

This is a Photizo example tutorial, using raw spatially resolved microspectroscopy data collected from 10 µm brain sections, where 3 are from cases with neurological disease and 3 are from controls. This data is available on Zenodo - to find more information about this and to view a list of required packages and versions, please see our github.

Load libraries

1.0 Pre-processing

2.0 Principal component analysis

AnnData assembly with spectral annotation

3.0 Clustering

Perform clustering

Explore other leiden resolutions and clinical data - ideal for inspection of batch effects

Save resolution of choice

4.0 Visualisation and quantification

Visualise cluster distribution across samples

Average the spectra of each cluster

Plot spectra in region of interest

Plot entire spectra per cluster

Quantification analysis

Mapping cluster classification